2.2 DNA extraction
The content of each capsule was transferred to a 50 mL Falcon tube that was centrifugated for 15 min at 15,000 g. The supernatant was removed, leaving 15 mL of liquid. Then, alcohol precipitation was performed by adding 33 mL of ethanol and 1.5 mL of 3M sodium acetate were added to each 50 mL tube, and samples were stored for 24h at -20°C. After centrifugation for 15 min at 15,000 g, the supernatant was discarded. 360 µL of ATL Buffer of the DNeasy Blood & Tissue Extraction Kit (Qiagen) were added to the pellet, thoroughly mixed, and transferred in a 2 mL tube. The remaining steps of the DNA extraction were carried out using the NucleoSpin soil kit (Macherey Nagel) from step 6. The DNA was eluted with 100 µL of SE buffer twice. Two types of extraction negative controls were performed during each extraction session, the first one starting with a 50 mL Falcon tube filled by CL1 buffer, and the second one starting with 360 µL of ATL Buffer of the DNeasy Blood & Tissue Extraction Kit (Qiagen) in a 2 mL tube.